readseq(1) Reads and writes nucleic/protein sequences in various formats


readseq [-options] in.seq > out.seq


This manual page documents briefly the readseq command. This manual page was written for the Debian GNU/Linux distribution because the original program does not have a manual page. Instead, it has documentation in text form, see below.

readseq reads and writes biosequences (nucleic/protein) in various formats. Data files may have multiple sequences. readseq is particularly useful as it automatically detects many sequence formats, and interconverts among them.


Formats which readseq currently understands:

  * IG/Stanford, used by Intelligenetics and others

  * GenBank/GB, genbank flatfile format

  * NBRF format

  * EMBL, EMBL flatfile format

  * GCG, single sequence format of GCG software

  * DNAStrider, for common Mac program

  * Fitch format, limited use

  * Pearson/Fasta, a common format used by Fasta programs and others

  * Zuker format, limited use. Input only.

  * Olsen, format printed by Olsen VMS sequence editor. Input only.

  * Phylip3.2, sequential format for Phylip programs

  * Phylip, interleaved format for Phylip programs (v3.3, v3.4)

  * Plain/Raw, sequence data only (no name, document, numbering)

  + MSF multi sequence format used by GCG software

  + PAUP's multiple sequence (NEXUS) format

  + PIR/CODATA format used by PIR

  + ASN.1 format used by NCBI

  + Pretty print with various options for nice looking output. Output only.

  + LinAll format, limited use (LinAll and ConStruct programs)

  + Vienna format used by ViennaRNA programs

See the included "Formats" file for detail on file formats.


Show summary of options.

Select All sequences

Change to lower case
Change to UPPER CASE

Remove gap symbols

Select Item number(s) from several

List sequences only

Redirect Output

Pipe (command line, <stdin, >stdout)

Change to Reverse-complement

Verbose progress

-f[ormat=]# Format number for output, or

    -f[ormat=]Name Format name for output:
    1. IG/Stanford           11. Phylip3.2       
    2. GenBank/GB            12. Phylip          
    3. NBRF                  13. Plain/Raw       
    4. EMBL                  14. PIR/CODATA      
    5. GCG                   15. MSF             
    6. DNAStrider            16. ASN.1           
    7. Fitch                 17. PAUP/NEXUS      
    8. Pearson/Fasta         18. Pretty (out-only)
    9. Zuker (in-only)       19. LinAll          
   10. Olsen (in-only)       20. Vienna          

Pretty format options:

Sequence line width

Left indent

Column space within sequence line on output

Count gap chars in sequence numbers

-nameleft, -nameright[=#]
Name on left/right side [=max width]

Name at top/bottom

-numleft, -numright
Seq index on left/right side

-numtop, -numbot
Index on top/bottom

Use match base for 2..n species

Blank line(s) between sequence blocks



      -- for interactive use

  readseq my.1st.seq  my.2nd.seq  -all  -format=genbank

      -- convert all of two input files to one genbank format output file

  readseq my.seq -all -form=pretty -nameleft=3 -numleft -numright -numtop -match

      -- output to standard output a file in a pretty format

  readseq my.seq -item=9,8,3,2 -degap -CASE -rev -f=msf -out=my.rev

      -- select 4 items from input, degap, reverse, and uppercase them

  cat *.seq | readseq -pipe -all -format=asn > bunch-of.asn

      -- pipe a bunch of data thru readseq, converting all to asn


This manual page was written by Stephane Bortzmeyer <[email protected]>, for the Debian GNU/Linux system (but may be used by others).